Sequence
atgc intronic sequence ATGC exonic sequencegtactaaaaaggttttagccacatttttgacaaaggtggatttgttttcgttctttattaccttgatttctgtgagattgatgatttctaccgtcttttctgtttgcagGAGAAGTGTTTCTAATCTACTACATAGTGGTTTCCGTGAAAGTCTTGATCAACTGATACAGTCATATGCTGAAAGGAGAGGACACACTCACGTAGACTGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G04460.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G04460.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G34240.1 (Glycine max), 3'ss of exon 6
gtactaaaaaggttttagccacatttttgacaaaggtggatttgttttcgttctttattaccttgatttctgtgagattgatgatttctaccgtcttttctgtttgcagGAGAAGTGTTTCTAATCTACTACATAGTGGTTTCCGTGAAAGTCTTGATCAACTGATACAGTCATATGCTGAAAGGAGAGGACACACTCACGTAGACTGG
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aaaatctaaatgagtatgccatttatacttca----tttattggctttcatttcttctagccaccaagcct-tatgattgtta---tggatttttattcatgttt-cagGAGAAGTGTTTCTAACCTTCTTCGTAGTGGTTTCCGTGAAAGTCTGGACCAACTAATACAGTCATATGTGGAAAGGCAAGGTCGTGCACCAATTGACTGG
upper sequence: AT5G04460.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G33300.1 (Glycine max), 3'ss of exon 5
gtactaaaaaggttttagccacatttttgacaaag-gtggatttgttttcgttctttattacc-ttgatttctgtgagattgatgatttctaccgtcttttctgtttgcagGAGAAGTGTTTCTAATCTACTACATAGTGGTTTCCGTGAAAGTCTTGATCAACTGATACAGTCATATGCTGAAAGGAGAGGACACACTCACGTAGACTGG
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--gtcgagattgtactga--acatggttgatacttcatttattggctttcatttcttcttgccaccaagccttattattgtatggattttta------ttcatgttt-cagGAGAAGTGTTTCTAACCTTCTTCGTAGTGGTTTCCGTGAAAGTCTGGACCAATTAATACAGTCATATGTGGAAAGGCAAGGTCGTGCACCAATTGACTGG
upper sequence: AT5G04460.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv13s0019g05390.t01 (Vitis vinifera), 3'ss of exon 3
gtactaaaaaggttttagccacatttttgacaaaggtggatttgttttcgttcttta-ttaccttgatttctgtgagattgatgatttctaccgtcttttctgtttgcagGAGAAGTGTTTCTAATCTACTACATAGTGGTTTCCGTGAAAGTCTTGATCAACTGATACAGTCATATGCTGAAAGGAGAGGACACACTCACGTAGACTGG
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------------------gtacttgattactgttagaaggccccttcacatcttttagttgccttttgctctggtaatttactca---atagtgggtttttttttggcagGAGAAGTGTCTCAAATCTTCTACGTAGTGGTTTTCGTGAGAGTTTAGACCAATTAATACAGTCATATGTGGAAAGGCAAGGTCGTGCGCCCATTGATTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattaccttgatttctgtgagattgatgatttctaccgtcttttctgtttgcagGAGAAGTGTTTCTAATCTACTACATAGTGGTTTCCGTGAAAGTCTTGATCAACTGATACAGTCATATGCTGAAAGGAGAGGACACACTCACGTAGACTGG
gattgat putative branch site (score: 4)
tttctaccgtcttttc putative PPT
ttgattt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactaaaaaggttttagccacatttttgacaaaggtggatttgttttcgttctttattaccttgatttctgtgagattgatgatttctaccgtcttttctgtttgcagGAGAAGTGTTTCTAATCTACTACATAGTGGTTTCCGTGAAAGTCTTGATCAACTGATACAGTCATATGCTGAAAGGAGAGGACACACTCACGTAGACTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA